turning fully rigged character into muscle capsules

Perhaps you could help me. I have fully rigged a biped character (with four arms and a tv for a head). Now I am trying to get some muscles going. When I convert the rig by going to Convert Smooth Skin to Muscle System, the joints do become capsules but the orientation is all wrong. I have changed each one to the appropriate x, y, or z axis, but they do not follow the path of the original bones. Therefore they don't join up from one end to the other.

How do I orient the capsules to the original bones without unskinning the character? Any thoughts? Thanks in advance.